Unraveling The Molecular Mechanisms Leading To The Fiber Quality Difference Between Gossypium Hirsutum And Gossypium Barbadense

Cotton is an important economic crop in China and the main source of natural textile fibers.Gossypium hirsutum and Gossypium barbadense are the main tetraploid domesticated species.They evolved from a common ancestor and have undergone through independent domestication.Gossypium hirsutum has good adaptability and the advantage of high yield.Gossypium barbadense produces fiber with better quality while the yield is low.The molecular mechanisms resulting in fiber quality differences formed during evolution and domestication between Gossypium hirsutum and Gossypium barbadense require further investigation.Here,we collected fiber samples from four Gossypium hirsutum cultivars(TM-1,4005,J220,XLZ42)and three Gossypium barbadense cultivars(Hai7124,R4-4,3-79)at different stages of fiber development,using transcriptome sequencing technology to compare the differences in gene expression in the process of fiber development from multiple dimensions.This study mapped the transcriptome sequencing data to the reference genomes,and compared the gene expression levels at different stages of fiber development in different cultivars.In most tissues of Gossypium hirsutum and Gossypium barbadense,some of the homologous genes of subgenomes showed the expression bias towards D subgenome.The overlapping genes with consistent expression bias patterns in four Gossypium hirsutum cultivars or three Gossypium barbadense cultivars were few,indicating that there was divergence in subgenome expression bias among different Gossypium hirsutum cultivars or Gossypium barbadense cultivars.Hierarchical cluster analysis further showed that the gene expression bias patterns of Gossypium hirsutum and Gossypium barbadense were divided into two main clusters.XLZ42 at 10 DPA and 3-79 at 20 DPA contained quite many unique genes that were expressed towards A or D subgenome.There were respectively 461 and 838 genes at 10 DPA and 20 DPA showing completely different expression bias patterns in fibers of Gossypium hirsutum and Gossypium barbadense,indicating that some genes related to fiber development have undergone functional differentiation during independent domestication.By comparing the tissue-specific and temporal differential expression patterns of genes in Gossypium hirsutum and Gossypium barbadense,we found that 703 genes were specifically expressed in TM-1 but not in Hai7124;623 genes were specifically expressed in Hai7124 but not in TM-1.In addition,6791 genes showed differential temporal expression patterns.In TM-1,346 genes were predominantly expressed at 10 DPA and postponed to 20 DPA in Hai7124;279 genes were predominantly expressed at 10 DPA and postponed to 25 DPA in Hai7124;367 genes were predominantly expressed at 20 DPA and postponed to 25 DPA in Hai7124.The 992 postponed genes were mapped to the KEGG pathway database and it turned out that these genes were widely involved in metabolic and regulatory pathways like galactose metabolism,sucrose and starch metabolism,gluconeogenesis/glycolysis,fatty acid metabolism and synthesis,and signal transduction of plant hormones.qRT-PCR verification of three important genes showed that their expression trends were consistent with the results from RNA-seq analysis.Through WGCNA analysis,key modules and hub genes corresponding to 10 DPA,20 DPA and 25 DPA were identified: In TM-1,10 DPA corresponded to the black module,which contained1013 genes and 101 transcription factors;20 DPA corresponded to the yellow module,which included 3700 genes and 211 transcription factors;25 DPA corresponded to the red module,which contained 1430 genes and 138 transcription factors.In Hai7124,10 DPA corresponded to the brown module,which contained 4948 genes and 189 transcription factors;20 DPA corresponded to the green module,which contained 2400 genes and 129 transcription factors;25 DPA corresponded to the blue module,which contained 5046 genes and 781 transcription factors.We further compared the distribution of hub genes of modules in Gossypium hirsutum and Gossypium barbadense,and found that three hub genes at 20 DPA in Hai7124 still corresponded to 20 DPA in TM-1,and owned a higher weight value(0.9～0.95);At 10 DPA,three hub genes in Hai7124 all corresponded to 5-10 DPA in TM-1,with a weight value of 0.87～0.95;at 25 DPA,the three hub genes in Hai7124 corresponded to 0-1 DPA,1 DPA and 5 DPA in TM-1,respectively.In general,this study used transcriptome sequencing to systematically compare the differences in homoeologous expression bias,temporal expression patterns of orthologs and coexpression regulatory network,and to identify key genes and molecular regulatory networks that cause the fiber quality difference between Gossypium hirsutum and Gossypium barbadense.This study could provide important genetic resources for cotton fiber improvement research in the future.